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tophat-fusion-post error when working with GRCh38 #59

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byb121 opened this issue Oct 9, 2019 · 0 comments
Open

tophat-fusion-post error when working with GRCh38 #59

byb121 opened this issue Oct 9, 2019 · 0 comments

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@byb121
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byb121 commented Oct 9, 2019

When using GRCh38 as the reference, some of our samples suffered the error below:

[Tue Sep 17 20:14:22 2019] Beginning TopHat-Fusion post-processing run (v2.1.0)
-----------------------------------------------
[Tue Sep 17 20:14:22 2019] Extracting 23-mer around fusions and mapping them using Bowtie
[Tue Sep 17 20:14:26 2019] Filtering fusions
	Processing: tophat_PR7519a.1/fusions.out
	Processing: tophat_PR7519a.10/fusions.out
	Processing: tophat_PR7519a.11/fusions.out
	Processing: tophat_PR7519a.12/fusions.out
	Processing: tophat_PR7519a.13/fusions.out
Ignoring: malformed coordinates:[ HLA-B*57:11:3016 ]
Ignoring: malformed coordinates:[ HLA-B*57:01:01:3016 ]
Ignoring: malformed coordinates:[ HLA-B*57:06:2963 ]
Ignoring: malformed coordinates:[ HLA-B*57:29:3016 ]
	Processing: tophat_PR7519a.14/fusions.out
Ignoring: malformed coordinates:[ HLA-DQB1*03:01:01:03:2499 ]
Ignoring: malformed coordinates:[ HLA-DQB1*03:01:01:01:2499 ]
Ignoring: malformed coordinates:[ HLA-DQB1*03:01:01:02:2498 ]
Ignoring: malformed coordinates:[ HLA-DQB1*03:01:01:03:2499 ]
Ignoring: malformed coordinates:[ HLA-DQB1*03:01:01:01:2499 ]
Ignoring: malformed coordinates:[ HLA-DQB1*03:01:01:02:2498 ]
	Processing: tophat_PR7519a.15/fusions.out
	Processing: tophat_PR7519a.16/fusions.out
	Processing: tophat_PR7519a.2/fusions.out
	Processing: tophat_PR7519a.3/fusions.out
	Processing: tophat_PR7519a.4/fusions.out
Traceback (most recent call last):
  File "/software/CGP/canpipe/live/bin/tophat-fusion-post", line 2927, in <module>
    sys.exit(main())
  File "/software/CGP/canpipe/live/bin/tophat-fusion-post", line 2898, in main
    filter_fusion(bwt_idx_prefix, params)
  File "/software/CGP/canpipe/live/bin/tophat-fusion-post", line 998, in filter_fusion
    filter_fusion_impl(fusion_file, junctions, refGene_list, ensGene_list, seq_chr_dic, fusion_gene_list)
  File "/software/CGP/canpipe/live/bin/tophat-fusion-post", line 804, in filter_fusion_impl
    chr, coord = chr_coord.split(':')
ValueError: too many values to unpack
Command exited with non-zero status 1
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